Determining the substrate specificity of a protease is essential for developing assays, inhibitors and understanding the mechanisms of the enzyme. In this work, we have profiled the specificity of Peptidyl-Lys metallopeptidase, (LysN), of Armillaria mellea, by a synthetic fluorescence resonance energy transfer (FRET) positional-scanning library. The library was based on a reference sequence K(Abz)-S-A-Q-K-M-V-S-K(Dnp), where the fluorescent donor is 2-aminobenzamide and the quencher is N-2,4-dinitrophenyl. Each position was varied between 19 different amino acids one by one, to reveal the specificity of the protease. LysN exhibits strict specificity for lysine in S1', and has less specificity moving further away from the scissile bond. Additivity between the subsites was observed and the best substrate identified was K(Abz)-M-R-F-K-R-R-R-K(Dnp) with a kcat/KM of 42.6 µM/s. Based on a homology structure model the reference substrate was fitted into the active site using molecular dynamics to propose peptide-enzyme interactions.

A method to express, purify and modify the PeptidylLys metallopeptidase (LysN) of Armillaria mellea in Pichia pastoris was developed to enable functional studies of the protease. Based on prior work, we propose a mechanism of action of LysN. Catalytic residues were investigated by site-directed mutagenesis. As anticipated, these mutations resulted in significantly reduced catalytic rates. Additionally, based on molecular modelling eleven mutants were designed to have altered substrate specificity. The S 1 0 binding pocket of LysN is quite narrow and lined with negative charge to specifically accommodate lysine. To allow for arginine specificity in S 1 0 , it was proposed to extend the S 1 0 binding pocket by mutagenesis, however the resulting mutant did not show any activity with arginine in P 1 0 . Two mutants, A101D and T105D, showed increased specificity towards arginine in subsites S 2 0 S 4 0 compared to the wild type protease. We speculate that the increased specificity to result from the additional negative charge which attract and interact with positively charged residues better than the wild type.Keywords: enzyme kinetics/enzyme mechanism/ metalloprotease/molecular modelling/site-directed mutagenesis.Abbreviations: Am-LysN, Armillaria mellea peptidyl-Lys metallopeptidase; DsbA, disulfideoxidoreductase; FRET, Fo¨rster resonance energy transfer; GAP, glyceraldehyde-3-phosphatedehydrogenase; IPTG, isopropylb-D-1-thiogalactopyranoside; MOE; Molecular Operation Environment (CCG); MOPS, 3-(N-morpholine)propanesulfonic acid; MS, mass spectrometry; PCR, polymerase chain reaction; RMSD, root-mean-square deviation; SDSPAGE, sodiumdodecylsulfatepolyacrylamide gel electrophoresis.In this article, we use Schechter and Berger nomenclature (1).Peptidyl-Lys metallopeptidase (LysN) from Armillaria mellea is an aspzincin metalloprotease, which cleaves in front of lysines (2). Hence, it is unusual by having its substrate specificity at the C-terminal side of the scissile bond (/K) (3). The protease is predominantly used as a tool in proteomic studies, where it serves as an alternative or complement to trypsin. The advantage of LysN is that it generates fragments which have a positive charge at the N-terminus, yielding mass spectrometry (MS) fragmentation with clear b-ion ladders (4,5). This feature can be used to facilitate de novo peptide mapping. Recently we profiled the substrate specificity of AmLysN and found it to be strictly lysine specific at S 1 0 , and having decreasing specificity when moving away from the scissile bond (2, 6).We also reported a homology model of Am-LysN based on the crystal structure of Gf-LysN (7). The two structures had a RMSD of 0.001 on backbone residues and 0.239 on the side chain residues (2). In this model Am-LysN has a narrow, and relatively short (57 amino acid) binding cleft. Central to the hydrolysis of peptides, is the zinc ion and the zinc binding motif 'HExxH + D'. Fushimi et al. showed that the aspartic acid D132 is necessary to coordinate zinc binding of the homologous protein ...

Adding fusion partners to proteins or peptides can aid or be a necessity to facilitate recombinant expression, folding, or purification. Independent of the reason it is desirable to remove the fusion partner to restore native functionality. Processing proteases catalyze the removal of fusion partners, however, most of these proteases have substrate specificity for the N-terminal of the scissile bond, leaving non-native termini if fusions are added to the C-terminal. The peptidyl-lys metallopeptidease of Armillaria mellea (Am-LysN) is unusual by having substrate specificity for the C-terminal side of the scissile peptide bond, allowing it to generate native C-termini. Am-LysN has strict specificity for lysine in P1', making all lysines of a protein or peptide a potential degradation site, however there are a number of amino acid side chains which lower hydrolysis significantly when located adjacent to the lysine. In this study we show that Am-LysN can be used as a processing protease to remove C-terminal extensions of peptides with no internal lysine to generate native Ctermini. Furthermore we show that removal of C-terminal extensions on peptides containing internal lysines can be achieved with little degradation of the product depending on the adjacent amino acids. These results demonstrate the utility of LysN allowing for novel ways to use fusion technology in the production of recombinant proteins.